Table S7. The consistency score under top 3, 5 and 7 reversal pairs in pair-wise datasets.
Dataset / 3 pairs / 5 pairs / 7 pairsGSE27262 / 0.9673 / 0.9696 / 0.9664
TCGA dataset / 0.9371 / 0.9399 / 0.9405
Table S8. Comparison of LncRIndiv and RankComp methods using simulation data.
|Log2FC*| / LncRIndiv / RankComp1.0 / F-score / 1.0000 / 0.9496
sensitivity / 1.0000 / 0.9080
specificity / 1.0000 / 0.9953
1.5 / F-score / 0.9842 / 0.9519
sensitivity / 0.9694 / 0.9102
specificity / 0.9995 / 0.9975
2.0 / F-score / 0.9916 / 0.9562
sensitivity / 0.9839 / 0.9200
specificity / 0.9995 / 0.9953
*FC denotes fold change.
Table S9.Information of lncRNAs with significant consistence between differential expression status and copy number alteration.
Ensembl_ID / Symbol / up/down / Copy number / ReferenceENSG00000177406.4 / RP11-218M22.1 / down / loss
ENSG00000177738.3 / CTD-2201E18.3 / up / gain
ENSG00000179523.4 / EIF3J-AS1 / down / loss
ENSG00000182873.4 / RP11-181G12.2 / down / loss
ENSG00000188206.5 / HNRNPU-AS1 / up / gain
ENSG00000196421.3 / LINC00176 / up / gain
ENSG00000215068.3 / AC025171.1 / up / gain
ENSG00000223393.1 / RP5-858B6.3 / up / gain
ENSG00000224032.2 / EPB41L4A-AS1 / down / loss / [1]
ENSG00000224660.1 / SH3BP5-AS1 / down / loss
ENSG00000226920.1 / RP5-1068B5.3 / up / gain
ENSG00000227502.2 / RP1-249H1.4 / down / loss
ENSG00000227533.1 / SLC2A1-AS1 / up / gain
ENSG00000228794.4 / RP11-206L10.11 / down / loss
ENSG00000228889.2 / UBAC2-AS1 / up / gain
ENSG00000229043.2 / AC091729.9 / up / gain
ENSG00000229152.1 / ANKRD10-IT1 / up / gain
ENSG00000229645.4 / LINC00341 / down / loss
ENSG00000230487.3 / PSMG3-AS1 / up / gain
ENSG00000230844.2 / ZNF674-AS1 / up / gain
ENSG00000232977.2 / LINC00327 / down / loss
ENSG00000233237.2 / LINC00472 / down / loss / [2]
ENSG00000233461.1 / RP11-295G20.2 / up / gain / [3]
ENSG00000233834.2 / AC005083.1 / up / gain
ENSG00000234286.1 / AC006026.13 / up / gain
ENSG00000234917.1 / RP5-994D16.3 / up / gain
ENSG00000235280.2 / MCF2L-AS1 / up / gain
ENSG00000235560.3 / AC002310.12 / up / gain
ENSG00000235770.1 / LINC00607 / down / loss
ENSG00000238005.2 / RP11-443B7.1 / up / gain
ENSG00000240859.1 / AC093627.10 / up / gain
ENSG00000241158.2 / ADAMTS9-AS1 / down / loss
ENSG00000241684.1 / ADAMTS9-AS2 / down / loss / [4]
ENSG00000245556.2 / CTD-2037K23.2 / down / loss
ENSG00000245711.2 / NADK2-AS1 / up / gain
ENSG00000247400.3 / DNAJC3-AS1 / up / gain
ENSG00000247498.5 / RP11-392P7.6 / down / loss
ENSG00000247556.2 / OIP5-AS1 / down / loss / [5]
ENSG00000248092.3 / NNT-AS1 / up / gain
ENSG00000248175.1 / CTC-428G20.3 / down / loss
ENSG00000249673.2 / NOP14-AS1 / down / loss
ENSG00000249700.4 / SRD5A3-AS1 / up / gain
ENSG00000250802.2 / ZBED3-AS1 / down / loss / [6]
ENSG00000253982.1 / CTD-2336O2.1 / down / loss
ENSG00000254703.2 / FLI1-AS1 / down / loss
ENSG00000255455.2 / RP11-890B15.3 / down / loss
ENSG00000258441.1 / LINC00641 / down / loss
ENSG00000258959.1 / RP11-1017G21.4 / down / loss
ENSG00000260219.1 / RP11-347C12.10 / up / gain
ENSG00000260279.1 / AC137932.5 / down / loss
ENSG00000260920.1 / RP1-228H13.5 / up / gain
ENSG00000261269.1 / RP11-389C8.2 / down / loss
ENSG00000261786.1 / RP4-555D20.2 / down / loss
ENSG00000261798.1 / RP1-118J21.25 / up / gain
ENSG00000261799.1 / RP11-283I3.6 / down / loss
ENSG00000264247.1 / LINC00909 / down / loss
ENSG00000268001.1 / CTC-241F20.3 / down / loss
ENSG00000268061.1 / NAPA-AS1 / down / loss
ENSG00000269940.1 / RP11-73M18.7 / down / loss
ENSG00000273015.1 / LINC00938 / down / loss
ENSG00000273356.1 / RP11-804H8.6 / down / loss
Table S10. Information of genes co-expressed with TMPO-AS1 and C1orf132 in cell cycle pathway in GSE50081.
lncRNA / Gene_Symbol / Gene ID / Direction# / T-test p_value / Pearson r / Pearson p_value / Reference*C1orf132 / CCND3 / 896 / down / 1.33E-06 / 0.61 / 4.97E-06 / [7]
C1orf132 / RBL2 / 5934 / down / 3.58E-03 / 0.73 / 3.04E-09 / [8]
TMPO-AS1 / CDC20 / 991 / up / 7.46E-06 / 0.48 / 4.14E-02 / [9]
TMPO-AS1 / CDC25A / 993 / up / 1.58E-05 / 0.51 / 3.25E-02 / [10]
TMPO-AS1 / ESPL1 / 9700 / up / 5.65E-04 / 0.61 / 7.32E-03 / [11]
TMPO-AS1 / MCM4 / 4173 / up / 1.95E-03 / 0.61 / 6.98E-03 / [12]
TMPO-AS1 / MCM7 / 4176 / up / 2.41E-03 / 0.58 / 1.22E-02 / [13]
TMPO-AS1 / MCM2 / 4171 / up / 2.75E-03 / 0.57 / 1.29E-02 / [14]
#The direction of genes mean up-regulation or down-regulation in the high-risk patient group compared with the low-risk patient group.
*The references reported the roles of genes related with cancer progression. The correlation of CCND3, RBL2, CDC20 and CDC25A with lung cancer have been described in the main text. The up-regulation of ESPL1 [11],MCM2[14], MCM7were significantly associated with poor prognosis for patients with non-small cell lung cancer [13]. Biological experiment showed that down-regulation of MCM4 reduced proliferation of non-small cell lung cancer cells [12].
Table S11.Differentially expressed lncRNAs of LUAD identified by LncRIndiv method supported by experimental evidence.
Ensemble ID / Symbol / up/down / ReferenceENSG00000180139.10 / ACTA2-AS1 / up / [15]
ENSG00000248771.1 / RP11-294O2.2 / up / [16]
ENSG00000242808.3 / SOX2-OT / up / [17]
ENSG00000224259.1 / RP11-48O20.4 / up / [18]
ENSG00000260940.1 / RP4-575N6.5 / down / [19]
ENSG00000261496.1 / RP13-514E23.1 / down / [19]
ENSG00000130600.11 / H19 / down / [20]
Table S12.Information of competing endogenous RNA and miRNA with the lncRNA C1orf132.
LncRNA / miRNA / Gene / miRNA-lncRNAsource database / miRNA-gene
source database
C1orf132 / hsa-miR-33a / CCND3 / mircode / miranda
C1orf132 / hsa-miR-16 / CCND3 / mircode / miranda;targetscan
C1orf132 / hsa-miR-370 / CCND3 / miranda / miranda
C1orf132 / hsa-miR-24 / CCND3 / mircode / miranda
C1orf132 / hsa-miR-7 / CCND3 / mircode / miranda
C1orf132 / hsa-miR-384 / CCND3 / miranda / miranda
C1orf132 / hsa-miR-1907 / CCND3 / mircode / targetscan
C1orf132 / hsa-miR-15a / CCND3 / mircode / miranda
C1orf132 / hsa-miR-506 / CCND3 / mircode / miranda;targetscan
C1orf132 / hsa-miR-124 / CCND3 / mircode / miranda;targetscan
C1orf132 / hsa-miR-497 / CCND3 / mircode / miranda;targetscan
C1orf132 / hsa-miR-15b / CCND3 / mircode / miranda
C1orf132 / hsa-miR-138 / CCND3 / mircode / miranda;targetscan
C1orf132 / hsa-miR-424 / CCND3 / mircode / miranda;targetscan
C1orf132 / hsa-miR-195 / CCND3 / mircode / miranda;targetscan
C1orf132 / hsa-miR-302e / RBL2 / mircode / miranda
C1orf132 / hsa-miR-106a / RBL2 / mircode / miranda
C1orf132 / hsa-miR-200a / RBL2 / mircode / miranda
C1orf132 / hsa-miR-340 / RBL2 / miranda / miranda;targetscan
C1orf132 / hsa-miR-17-5p / RBL2 / mircode / mirtarbase;targetscan
C1orf132 / hsa-miR-20b / RBL2 / mircode / miranda
C1orf132 / hsa-miR-370 / RBL2 / miranda / miranda
C1orf132 / hsa-miR-373 / RBL2 / mircode / miranda
C1orf132 / hsa-miR-302a / RBL2 / mircode / miranda
C1orf132 / hsa-miR-129-5p / RBL2 / mircode / miranda
C1orf132 / hsa-miR-302b / RBL2 / mircode / miranda
C1orf132 / hsa-miR-141 / RBL2 / mircode / miranda
C1orf132 / hsa-miR-20a / RBL2 / mircode / miranda
C1orf132 / hsa-miR-106b / RBL2 / mircode / miranda
C1orf132 / hsa-miR-107 / RBL2 / mircode / miranda
C1orf132 / hsa-miR-204 / RBL2 / mircode / miranda
C1orf132 / hsa-miR-211 / RBL2 / mircode / miranda
C1orf132 / hsa-miR-93 / RBL2 / mircode / miranda;targetscan
C1orf132 / hsa-miR-519d / RBL2 / mircode / miranda;targetscan
C1orf132 / hsa-miR-17 / RBL2 / mircode / miranda
C1orf132 / hsa-miR-372 / RBL2 / mircode / miranda
C1orf132 / hsa-miR-520e / RBL2 / mircode / miranda
C1orf132 / hsa-miR-302c / RBL2 / mircode / miranda
C1orf132 / hsa-miR-520b / RBL2 / mircode / miranda
C1orf132 / hsa-miR-302d / RBL2 / mircode / miranda
Table S13. Sensitivity, specificity, and F-score in simulated data under different scenarios.
Sample Number / 210 vs 210 / 60 vs 60|Log2FC*| / Grade# / F-score / Sensitivity / Specificity / F-score / Sensitivity / Specificity
1.0 / 10 / 1.0000 / 1.0000 / 1.0000 / 0.9800 / 0.9639 / 0.9967
20 / 0.8527 / 0.7445 / 0.9978 / 0.8239 / 0.7019 / 0.9973
30 / 0.8368 / 0.7206 / 0.9978 / 0.7673 / 0.6229 / 0.9987
1.5 / 10 / 0.9842 / 0.9694 / 0.9995 / 0.976 / 0.9548 / 0.9982
20 / 0.9209 / 0.8552 / 0.9975 / 0.9102 / 0.8365 / 0.9982
30 / 0.8931 / 0.8081 / 0.998 / 0.8696 / 0.7699 / 0.999
2.0 / 10 / 0.9916 / 0.9839 / 0.9995 / 0.9872 / 0.9748 / 1.0000
20 / 0.9611 / 0.9272 / 0.9975 / 0.9629 / 0.9296 / 0.9987
30 / 0.9560 / 0.9173 / 0.9980 / 0.9520 / 0.9093 / 0.9990
*FC denotes fold change.
#denotes the number of disease samples in which a DE lncRNA was simulated to be differentially expressed.
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